cancervariants / disease-normalization

Services and guidelines for normalizing disease terms
https://disease-normalizer.readthedocs.io/latest/
MIT License
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All mondo xrefs are broken #197

Open jsstevenson opened 3 months ago

jsstevenson commented 3 months ago

Describe the bug

No mondo xrefs :(

Steps to reproduce

disease_norm_update --update_all --update_merged

Expected behavior

there should be xrefs

Current behavior

    "Mondo": {
      "match_type": 60,
      "records": [
        {
          "label": "leukemia, acute lymphocytic, susceptibility to, 1",
          "concept_id": "mondo:0013108",
          "aliases": [
            "ALL",
            "leukemia, acute lymphoblastic, B-Hyperdiploid, susceptibility to",
            "leukemia, acute lymphoblastic, susceptibility to, 1",
            "leukemia, B-cell acute lymphoblastic, susceptibility to",
            "leukemia, T-cell acute lymphoblastic, susceptibility to",
            "All1",
            "leukemia, T-cell acute lymphoblastic, somatic",
            "leukemia, acute lymphoblastic, somatic",
            "T-cell acute lymphoblastic leukemia, somatic",
            "leukemia, acute lymphoblastic",
            "leukemia, acute lymphocytic, susceptibility to, 1",
            "leukemia, acute lymphocytic, Philadelphia chromosome positive, somatic",
            "leukemia, T-cell acute lymphocytic, somatic"
          ],
          "xrefs": [],
          "associated_with": []
        }
      ],
      "source_meta_": {
        "data_license": "CC BY 4.0",
        "data_license_url": "https://creativecommons.org/licenses/by/4.0/legalcode",
        "version": "20240702",
        "data_url": "https://mondo.monarchinitiative.org/pages/download/",
        "rdp_url": "http://reusabledata.org/monarch.html",
        "data_license_attributes": {
          "non_commercial": false,
          "share_alike": false,
          "attribution": true
        }
      }
    }

Possible reason(s)

No response

Suggested fix

No response

Branch, commit, and/or version

bf11f7a

Screenshots

No response

Environment details

mac

Additional details

No response

Contribution

Yes, I can create a PR for this fix.

github-actions[bot] commented 3 weeks ago

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